AO3 is probably the most comprehensive for 'NaruNeji' content these days. The tagging system there is a lifesaver; you can filter by pairing, word count, kudos, and even specific tropes like 'Friends to Lovers' or 'Alternate Universe - No Chūnin Exams'. I've found some incredibly well-written, novel-length fics that explore their dynamic post-war, which you don't see as much on other sites. FF.net still has a massive archive of older stories from the mid-2000s golden age of Naruto fandom, but sorting through them can be a chore without the same level of tag refinement. Honestly, I've had better luck with character-driven pieces on AO3 lately.
That said, don't completely ignore smaller forums or LiveJournal communities that might be archived. Some of the most poignant one-shots I've read were buried in threads on 'narutoyaoi' communities from 2008. The writing style is different—less polished sometimes, but it has this raw, passionate energy that's really nostalgic. Tumblr also hosts a lot of modern micro-fics and headcanon posts under the #naruneji tag, which is great for quick reads and visual moodboards.